The complete plastid genome sequence of Lysidice brevicalyx (Fabaceae: Detarioideae), an arbor species endemic to China

Abstract The plastid genome of Lysidice brevicalyx was successfully assembled using Illumina sequencing reads for the first time. The complete plastid genome of L. brevicalyx is a circular structure of 159,084 bp with a GC content of 36.4%. It comprises a large single-copy (LSC) region of 87,783 bp, a small single-copy (SSC) region of 19,557 bp, and two inverted repeat regions (IRA and IRB) of 25,872 bp, each. The plastome of L. brevicalyx contains a total of 128 genes, including 83 protein-coding genes, 37 tRNAs, and 8 rRNAs. The phylogenetic analysis strongly supports the monophyly of Lysidice. This study provides the first complete plastid genome sequence of L. brevicalyx and contributes to our understanding of the molecular characteristics and evolutionary relationships of this plant species.


Introduction
The genus Lysidice (Fabaceae) consists of two species, viz.Lysidice rhodostegia Hance 1867 from China and Vietnam and Lysidice brevicalyx C. F. Wei 1983 endemic to southern China (Hou 2010).L. brevicalyx is a valuable tree species used for building materials due to its white-yellow wood (Figure 1) and has been used as an alternative medicine for the treatment of fractures and traumatic bleeding in China (Gao et al. 2007).Additionally, the roots, stems, and leaves of L. brevicalyx have been used for medicinal purposes by local communities (Wu et al. 2010, Yang et al. 2019).In this study, we report the first assembly and annotation of the complete plastid genome of L. brevicalyx (Figure 2) using second-generation sequencing technology.

Materials and methods
Fresh leaves of L. brevicalyx were collected from the South China Botanical Garden in Guangzhou City, Guangdong Province, China (N 23 � 11'12.62 0 ', E 113 � 21'51.15 0').A voucher specimen (Q.Lai LaiQ036) was deposited in IBSC (contact person: Qiang Lai, laiqiang@scbg.ac.cn).Total genomic DNA was extracted from the fresh leaves using a combination of the improved cetyltrimethylammonium bromide (CTAB) method (Doyle andDoyle 1987, Yang et al. 2014) and the Dneasy Plant Mini Kit extraction.Quality monitoring was performed using a Qubit 3.0 fluorometer.Genomic DNA was sheared to prepare a PCR-free library with an insert size of 150 bp.High-throughput sequencing was conducted using the Illumina Hiseq X-Ten system, generating a total of 2.3 GB of pair-end reads.The plastid genome was assembled using the GetOrganelle v1.7.7.0 (Jin et al. 2020), and the unique genes of the L. brevicalyx plastid genome were annotated using CPGAVAS2 web service (Shi et al. 2019).A gene graphical map of the plastid genome was constructed using CPGVIEW (http://www.1kmpg.cn/cpgview) (Liu et al. 2023).Then final plastid genome of L. brevicalyx was submitted to NCBI Gene Bank with an accession number of OQ808806.Firstly, a total of 19 plastid genomes were downloaded from NCBI Gene Bank, 74 protein-coding genes shared by all genomes were screened.Subsequently, MAFFT v7.313 (Katoh et al. 2019) was used for separate alignment of each gene, and maximum likelihood phylogenies were inferred using IQ-TREE (Minh et al. 2022)

Results and discussion
The newly assembled plastid genome of Lysidice brevicalyx is 159,084 bp in length.The sequencing coverage depths of the genome ranged from 73 to 18733 with a mean coverage depth of 1195.943,indicating the reliability of the genome assembly.The plastid gene structure of L. brevicalyx is a circular molecule (Figure 2), consisting of four parts: a large single-copy region (LSC) of 87,783 bp, a small single-copy region (SSC) of 19,557 bp, and two inverted repeat regions (IRA and IRB), each 25,872 bp.The plastome contains a total of 128 genes, including 83 protein-coding genes, 37 tRNAs, 8 rRNAs.Among the protein-coding genes, 14 protein-coding genes  (atpF, ndhA, ndhB, petB, petD, rpl16, rpoC1, rps16, trnA-UGC, trnG-UCC, trnI-GAU, trnK-UUU, trnL-UAA, and trnV-UAC) contain one intron and three genes (clpP, rps12, and ycf3) have two introns.Three small-exon genes (petB, petD, and rps16) and one trans-spliced gene (rps12) were verified to be corrected and annotated with multiple sequence alignment.
For the construction of the Maximum Likelihood (ML) phylogenetic tree, a total of 19 complete plastid genomes of fabales were used (Figure 3).The result showed that L. brevicalyx is closely related to L. rhodostegia, Afzelia xylocarpa (Kurz) Craib, and Crudia harmsiana De Wil, and all of them formed a clade with high supported value (BP ¼ 100%).These findings are consistent with previous research (Zhao et al. 2021)

Conclusion
This study presents the first report of the plastid genome of Lysidice brevicalyx, and adds to the limited number of plastid genomes reported for the genus Lysidice.The phylogenetic analysis revealed that Lysidice forms an independent sister clade to other species, providing novel insights into the phylogenetic relationships within the Leguminosae family.The genetic resource information generated in this study will be valuable for further investigations into the biology and evolutionary history of Lysidice.

Figure 1 .
Figure 1.Plant image of Lysidice brevicalyx.The image showing flowers are actinomorphic, with purple flag and wing petals, an evenly pinnate leaf, flattened, twisted pods.This photo was taken by youpai zeng.

Figure 2 .
Figure 2. Gene map of the plastid genome of Lysidice brevicalyx.From the center outward, the first track indicates the dispersed repeats; the second track shows the long tandem repeats as short blue bars; the third track shows the short tandem repeats or microsatellite sequences as short bars with different colors; the fourth track shows small single-copy (SSC), inverted repeat (IRA and IRB), and large single-copy (LSC) regions.The GC content along the genome is plotted on the fifth track; the genes are shown on the sixth track.
. The clade comprising subfamilies Cercidoideae and Detarioideae is sister to the remaining legumes, and Duparquetioideae and Dialioideae are successive sisters to the clade of Papilionoideae and Caesalpinioideae.